LOMAR (version 0.5.0)

locs_from_csv: locs_from_csv

Description

Reads and filters single molecule localization events from a csv file as typically output by the SMAP software. The main columns of interest are the coordinates (x, y, z), point set membership (site) and localization precision (locprec and locprecz).

Usage

locs_from_csv(
  file = NULL,
  roi = NULL,
  channels = NULL,
  frame.filter = NULL,
  llrel.filter = NULL,
  locprec.filter = 0,
  locprecz.filter = 0
)

Value

a data frame with columns x,y,z, optionally site, locprec and locprecz.

Arguments

file

a csv file with columns x[nm], y[nm], z[nm] and optionally site[numbers], channel, locprec[nm] and locprecz[nm], other columns are ignored.

roi

region of interest, keep points within the specified volume. Must be a data frame with columns x,y,z and rows min and max defining a bounding box.

channels

vector of integers indicating which channel(s) of a multicolour experiment to get data from.

frame.filter

vector of min and max values, filter out points from frames outside the specified range.

llrel.filter

vector of min and max values, filter out points on log-likelihood (for fitted data).

locprec.filter

filter out points with locprec value greater than the specified number. Points with locprec == 0 are also removed.

locprecz.filter

filter out points with locprecz value greater than the specified number. Points with locprecz == 0 are also removed.

Examples

data.file <- system.file("test_data", "simulated_NUP107_data.csv", package = "LOMAR",
 mustWork = TRUE)
locs <- locs_from_csv(file = data.file, locprec.filter = 20)